Atomistic structure simulation of silicon nanocrystals driven with suboxide penalty energies

The structural control of silicon nanocrystals embedded in amorphous oxide is currently an important technological problem. In this work, an approach is presented to simulate the structural behavior of silicon nanocrystals embedded in amorphous oxide matrix based on simple valence force fields as described by Keating-type potentials. After generating an amorphous silicon-rich-oxide, its evolution towards an embedded nanocrystal is driven by the oxygen diffusion process implemented in the form of a Metropolis algorithm based on the suboxide penalty energies. However, it is observed that such an approach cannot satisfactorily reproduce the shape of annealed nanocrystals. As a remedy, the asphericity and surface-to-volume minimization constraints are imposed. With the aid of such a multilevel approach, realistic-sized silicon nanocrystals can be simulated. Prediction for the nanocrystal size at a chosen oxygen molar fraction matches reasonably well with the experimental data when the interface region is also accounted. The necessity for additional shape constraints suggests the use of more involved force fields including long-range forces as well as accommodating different chemical environments such as the double bonds. Copyright © 2008 American Scientific Publishers All rights reserved

Brownian Motors driven by Particle Exchange

We extend the Langevin dynamics so that particles can be exchanged with a particle reservoir. We show that grand canonical ensembles are realized at equilibrium and derive the relations of thermodynamics for processes between equilibrium states. As an application of the proposed evolution rule, we devise a simple model of Brownian motors driven by particle exchange. KEYWORDS: Langevin Dynamics, Thermodynamics, Open SystemsComment: 5 pages, late

Caltech Asci Technical Report 110

The recent advent of inexpensive commodity multiprocessor computers with standardized operating system support for lightweight threads provides computational chemists and other scientists with an exciting opportunity to develop sophisticated new approaches to materials simulation. We contrast the flexible performance characteristics of lightweight threading with the restrictions of traditional scientific supercomputing, based on our experiences with multithreaded molecular dynamics simulation. Motivated by the results of our molecular dynamics experiments, we propose an approach to multi-scale materials simulation using highly dynamic thread creation and synchronization within and between concurrent simulations at many different scales. This approach will enable extremely realistic simulations, with computing resources dynamically directed to areas where they are needed. Multi-scale simulations of this kind require large amounts of processing power, but are too sophisticated to be expressed using traditional supercomputing programming models. As a result, we have developed a high-level programming system called Sthreads that allows highly dynamic, nested multithreaded algorithms to be expressed. Program development is simplified through the use of innovative synchronization operations that allow multithreaded programs to be tested and debugged using standard sequential methods and tools. For this reason, Sthreads is very well suited to the complex multi-scale simulation applications that we are developing